The money from the Department of Health is to cover costs until the end of the financial year.
Peterborough and Stamford Hospitals NHS Foundation Trust's debt has risen to more than £56m.
Peterborough City Hospital opened in 2010 and was funded by a Private Finance Initiative (PFI).
The £46m is in addition to a government bailout for hospital trusts struggling to pay PFI debts, which was announced on 3 February.
It costs the trust £3m a month to pay back its PFI debt.
Peter Reading, interim chief executive of Peterborough and Stamford Hospitals NHS Foundation Trust, said it is "extremely positive news for the trust."